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Open data
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Basic information
Entry | Database: PDB / ID: 6spl | ||||||
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Title | Fragment KCL615 in complex with MAP kinase p38-alpha | ||||||
![]() | Mitogen-activated protein kinase 14![]() | ||||||
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Function / homology | ![]() DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence ...DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nichols, C.E. / De Nicola, G.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 ...Title: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes. Authors: Nichols, C. / Ng, J. / Keshu, A. / Kelly, G. / Conte, M.R. / Marber, M.S. / Fraternali, F. / De Nicola, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.5 KB | Display | ![]() |
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PDB format | ![]() | 70.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5r85C ![]() 5r86C ![]() 5r87C ![]() 5r88C ![]() 5r89C ![]() 5r8aC ![]() 5r8bC ![]() 5r8cC ![]() 5r8dC ![]() 5r8eC ![]() 5r8fC ![]() 5r8gC ![]() 5r8hC ![]() 5r8iC ![]() 5r8jC ![]() 5r8kC ![]() 5r8lC ![]() 5r8mC ![]() 5r8nC ![]() 5r8oC ![]() 5r8pC ![]() 5r8qC ![]() 5r8uC ![]() 5r8vC ![]() 5r8wC ![]() 5r8xC ![]() 5r8yC ![]() 5r8zC ![]() 5r90C ![]() 5r91C ![]() 5r92C ![]() 5r93C ![]() 5r94C ![]() 5r95C ![]() 5r96C ![]() 5r97C ![]() 5r98C ![]() 5r99C ![]() 5r9aC ![]() 5r9bC ![]() 5r9cC ![]() 5r9dC ![]() 5r9eC ![]() 5r9fC ![]() 5r9gC ![]() 5r9hC ![]() 5r9iC ![]() 5r9jC ![]() 5r9kC ![]() 5r9lC ![]() 5r9mC ![]() 5r9nC ![]() 5r9oC ![]() 5r9pC ![]() 5r9qC ![]() 5r9rC ![]() 5r9sC ![]() 5r9tC ![]() 5r9uC ![]() 5r9vC ![]() 5r9wC ![]() 5r9xC ![]() 5r9yC ![]() 5r9zC ![]() 5ra0C ![]() 5ra1C ![]() 5ra2C ![]() 5ra3C ![]() 5ra4C ![]() 5ra5C ![]() 5ra6C ![]() 5ra7C ![]() 5ra8C ![]() 5ra9C ![]() 6so1C ![]() 6so2C ![]() 6so4C ![]() 6sodC ![]() 6soiC ![]() 6sotC ![]() 6souC ![]() 6sovC ![]() 6sp9SC ![]() 6y7wC ![]() 6y7xC ![]() 6y7yC ![]() 6y80C ![]() 6y81C ![]() 6ycuC ![]() 6ycwC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 41379.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P47811, ![]() |
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-Non-polymers , 5 types, 276 molecules ![](data/chem/img/SB4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LOW.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LOW.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SB4 / | ||||||
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#3: Chemical | #4: Chemical | ![]() #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.46 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 15% PEG400, 5% PEG550-MME, 0.1M calcium acetate, 0.1M MES pH6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.38→72.85 Å / Num. obs: 87933 / % possible obs: 99.72 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4259 / CC1/2: 0.642 / % possible all: 97.62 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6SP9 Resolution: 1.38→72.85 Å / SU ML: 0.1945 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.2826
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→72.85 Å
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Refine LS restraints |
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LS refinement shell |
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